Plant adaptation or acclimation to rising CO2 ? Insight from first multigenerational RNA-Seq transcriptome

Design and Characterization of a Transcriptional Repression Toolkit for Plants

Regulation of gene expression is essential for all life. Tools to manipulate the gene expression level have therefore proven to be very valuable in efforts to engineer biological systems. However, there are few well-characterized genetic parts that reduce gene expression in plants, commonly known as transcriptional repressors. We characterized the repression activity of a library consisting of repression motifs from approximately 25% of the members of the largest known family of repressors. Combining sequence information with our trans-regulatory function data, we next generated a library of synthetic transcriptional repression motifs with function predicted in advance. After characterizing our synthetic library, we demonstrated not only that many of our synthetic constructs were functional as repressors but also that our advance predictions of repression strength were better than random guesses. Finally, we assessed the functionality of known transcriptional repression motifs from a wide range of eukaryotes. Our study represents the largest plant repressor motif library experimentally characterized to date, providing unique opportunities for tuning transcription in plants.

Response of Fragaria vesca to projected change in temperature, water availability and concentration of CO2 in the atmosphere

The high rate of climate change may soon expose plants to conditions beyond their adaptation limits. Clonal plants might be particularly affected due to limited genotypic diversity of their populations, potentially decreasing their adaptability. We therefore tested the ability of a widely distributed predominantly clonally reproducing herb (Fragaria vesca) to cope with periods of drought and flooding in climatic conditions predicted to occur at the end of the twenty-first century, i.e. on average 4 °C warmer and with twice the concentration of CO2 in the air (800 ppm) than the current state. We found that F. vesca can phenotypically adjust to future climatic conditions, although its drought resistance may be reduced. Increased temperature and CO2 levels in the air had a far greater effect on growth, phenology, reproduction, and gene expression than the temperature increase itself, and promoted resistance of F. vesca to repeated flooding periods. Higher temperature promoted clonal over sexual reproduction, and increased temperature and CO2 concentration in the air triggered change in expression of genes controlling the level of self-pollination. We conclude that F. vesca can acclimatise to predicted climate change, but the increased ratio of clonal to sexual reproduction and the alteration of genes involved in the self-(in)compatibility system may be associated with reduced genotypic diversity of its populations, which may negatively impact its ability to genetically adapt to novel climate in the long-term.

Genomic insights into genetic diversity and local adaptation of a dominant desert steppe feather grass, Stipa breviflora Griseb

Investigating the genetic mechanisms of local adaptation is critical to understanding how species adapt to heterogeneous environments. In the present study, we analyzed restriction site-associated DNA sequencing (RADseq) data in order to explore genetic diversity, genetic structure, genetic differentiation, and local adaptation of Stipa breviflora. In total, 135 individual plants were sequenced and 25,786 polymorphic loci were obtained. We found low genetic diversity (He = 0.1284) within populations of S. breviflora. Four genetic clusters were identified along its distribution range. The Mantel test, partial Mantel test, and multiple matrix regression with randomization (MMRR) indicate that population differentiation was caused by both geographic distance and environmental factors. Through the F_ST outlier test and environmental association analysis (EAA), 113 candidate loci were identified as putatively adaptive loci. RPK2 and CPRF1, which are associated with meristem maintenance and light responsiveness, respectively, were annotated. To explore the effects of climatic factors on genetic differentiation and local adaptation of S. breviflora, gradient forest (GF) analysis was applied to 25,786 single nucleotide polymorphisms (SNPs) and 113 candidate loci, respectively. The results showed that both temperature and precipitation affected the genetic differentiation of S. breviflora, and precipitation was strongly related to local adaptation. Our study provides a theoretical basis for understanding the local adaptation of S. breviflora.

Effects of three patterns of elevated CO2 in single and multiple generations on photosynthesis and stomatal features in rice

BACKGROUND AND AIMS

Effects of elevated CO2 (E) within a generation on photosynthesis and stomatal features have been well documented in crops; however, long-term responses to gradually elevated CO2 (Eg) and abruptly elevated CO2 (Ea) over multiple generations remain scarce.

METHODS

Japonica rice plants grown in open-top chambers were tested in the first generation (F1) under Ea and in the fifth generation (F5) under Eg and Ea, as follows: Ea in F1: ambient CO2 (A) + 200 μmol mol-1; Eg in F5: an increase of A + 40 μmol mol-1 year-1 until A + 200 μmol mol-1 from 2016 to 2020; Ea in F5: A + 200 μmol mol-1 from 2016 to 2020. For multigenerational tests, the harvested seeds were grown continuously in the following year in the respective CO2 environments.

KEY RESULTS

The responses to Ea in F1 were consistent with the previous consensus, such as the occurrence of photosynthetic acclimation, stimulation of photosynthesis, and downregulation of photosynthetic physiological parameters and stomatal area. In contrast, multigenerational exposure to both Eg and Ea did not induce photosynthetic acclimation, but stimulated greater photosynthesis and had little effect on the photosynthetic physiology and stomatal traits. This suggests that E retained intergenerational effects on photosynthesis and stomatal features and that there were no multigenerational differences in the effects of Eg and Ea.

CONCLUSIONS

The present study demonstrated that projecting future changes induced by E based on the physiological responses of contemporary plants could be misleading. Thus, responses of plants to large and rapid environmental changes within a generation cannot predict the long-term response of plants to natural environmental changes over multiple generations, especially in annual herbs with short life cycles.

The functional significance of the stomatal size to density relationship: Interaction with atmospheric [CO2] and role in plant physiological behaviour

The limits for stomatal conductance are set by stomatal size (SS) and density (SD). An inverse relationship between SS and SD has been observed in fossil and living plants. This has led to hypotheses proposing that the ratio of SS to SD influences the diffusion pathway for CO₂ and degree of physiological stomatal control. However, conclusive evidence supportive of a functional role of the SS-SD relationship is not evident, and patterns in SS-SD may simply reflect geometric constraints in stomatal spacing over a leaf surface. We examine published and new data to investigate the potential functional significance of the relationship between SS and SD to atmospheric [CO₂] in multiple generation adaptive responses and short-term acclamatory adjustment of stomatal morphology. Consistent patterns in SS and SD were not evident in fossil and living plants adapted to high [CO₂] over many generations. However, evolutionary adaptation to [CO₂] strongly affected SS and SD responses to elevated [CO₂], with plants adapted to the 'low' [CO₂] of the past 10 million years (Myr) showing adjustment of SS-SD, while members of the same species adapted to 'high' [CO₂] showed no response. This may suggest that SS and SD responses to future [CO₂] will likely constrain the stimulatory effect of 'CO₂-fertilisation' on photosynthesis. Angiosperms generally possessed higher densities of smaller stomata that corresponded to a greater degree of physiological stomatal control consistent with selective pressures induced by declining [CO₂] over the past 90 Myr. Atmospheric [CO₂] has likely shaped stomatal size and density relationships alongside the interaction with stomatal physiological behaviour. The rate and predicted extent of future increases in [CO₂] will have profound impacts on the selective pressures shaping SS and SD. Understanding the trade-offs involved in SS-SD and the interaction with [CO₂], will be central to the development of more productive climate resilient crops.

G protein γ subunit qPE9-1 is involved in rice adaptation under elevated CO2 concentration by regulating leaf photosynthesis

G protein γ subunit qPE9-1 plays multiple roles in rice growth and development. However, the role of qPE9-1 in rice exposed to elevated carbon dioxide concentration (eCO₂) is unknown. Here, we investigated its role in the regulation of rice growth under eCO₂ conditions using qPE9-1 overexpression (OE) lines, RNAi lines and corresponding WT rice. Compared to atmospheric carbon dioxide concentration (aCO₂), relative expression of qPE9-1 in rice leaf was approximately tenfold higher under eCO₂. Under eCO₂, the growth of WT and qPE9-1-overexpressing rice was significantly higher than under aCO₂. Moreover, there was no significant effect of eCO₂ on the growth of qPE9-1 RNAi lines. Furthermore, WT and qPE9-1-overexpressing rice showed higher net photosynthetic rate and carbohydrate content under eCO₂ than under aCO₂. Moreover, the relative expression of some photosynthesis related genes in WT, but not in RNAi3 line, showed significant difference under eCO₂ in RNA-seq analysis. Compared to WT and RNAi lines, the rbcL gene expression and Rubisco content of rice leaves in qPE9-1-overexpressors were higher under eCO₂. Overall, these results suggest that qPE9-1 is involved in rice adaptation under elevated CO₂ concentration by regulating leaf photosynthesis via moderating rice photosynthetic light reaction and Rubisco content.

Relationship between endophytic microbial diversity and grain quality in wheat exposed to multi-generational CO2 elevation

To explore the potential association between the diversity of endophytic microorganisms and modifications of grain quality in wheat exposed to multi-generational elevated CO₂ concentration, the grain quality attributes and microbial diversity were tested after five generations successively grown in ambient CO₂ concentration (F5_A, 400 μmol L^-1) and elevated CO₂ concentration (F5_E, 800 μmol L^-1). Elevated CO₂ concentration significantly increased the grain number and starch concentration, while decreased the grain protein concentration. Multi-generational exposure to elevated CO₂ concentration also led to significant changes in grain amino acid concentration. In response to the elevated CO₂ concentration, Pseudomonas, Rhodococcus, Ralstonia, and Klebsiella were the dominant bacterial genera, while Penicillium, Cutaneotrichosporon, Fusarium, Sarocladium, Acremonium and Aspergillus were the dominant fungal genera in wheat grain. A significantly positive correlation was found between Pseudomonas, Penicillium and ratio of starch to protein concentration, implying that the multi-generational CO₂ elevation induced modifications in grain quality might be associated with the changes in grain microbial diversity. The results of this study suggest that the endophytic microbes may play an important role in modulating the grain nutritional quality in wheat under multi-generational e[CO₂] exposure, through regulating starch and N metabolism and production of secondary metabolites.

Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival

Coastal oceans are particularly affected by rapid and extreme environmental changes with dramatic consequences for the entire ecosystem. Seagrasses are key ecosystem engineering or foundation species supporting diverse and productive ecosystems along the coastline that are particularly susceptible to fast environmental changes. In this context, the analysis of phenotypic plasticity could reveal important insights into seagrasses persistence, as it represents an individual property that allows species' phenotypes to accommodate and react to fast environmental changes and stress. Many studies have provided different definitions of plasticity and related processes (acclimation and adaptation) resulting in a variety of associated terminology. Here, we review different ways to define phenotypic plasticity with particular reference to seagrass responses to single and multiple stressors. We relate plasticity to the shape of reaction norms, resulting from genotype by environment interactions, and examine its role in the presence of environmental shifts. The potential role of genetic and epigenetic changes in underlying seagrasses plasticity in face of environmental changes is also discussed. Different approaches aimed to assess local acclimation and adaptation in seagrasses are explored, explaining strengths and weaknesses based on the main results obtained from the most recent literature. We conclude that the implemented experimental approaches, whether performed with controlled or field experiments, provide new insights to explore the basis of plasticity in seagrasses. However, an improvement of molecular analysis and the application of multi-factorial experiments are required to better explore genetic and epigenetic adjustments to rapid environmental shifts. These considerations revealed the potential for selecting the best phenotypes to promote assisted evolution with fundamental implications on restoration and preservation efforts.

Integrating stomatal physiology and morphology: evolution of stomatal control and development of future crops

Stomata are central players in the hydrological and carbon cycles, regulating the uptake of carbon dioxide (CO₂) for photosynthesis and transpirative loss of water (H₂O) between plants and the atmosphere. The necessity to balance water-loss and CO₂-uptake has played a key role in the evolution of plants, and is increasingly important in a hotter and drier world. The conductance of CO₂ and water vapour across the leaf surface is determined by epidermal and stomatal morphology (the number, size, and spacing of stomatal pores) and stomatal physiology (the regulation of stomatal pore aperture in response to environmental conditions). The proportion of the epidermis allocated to stomata and the evolution of amphistomaty are linked to the physiological function of stomata. Moreover, the relationship between stomatal density and [CO₂] is mediated by physiological stomatal behaviour; species with less responsive stomata to light and [CO₂] are most likely to adjust stomatal initiation. These differences in the sensitivity of the stomatal density—[CO₂] relationship between species influence the efficacy of the ‘stomatal method’ that is widely used to infer the palaeo-atmospheric [CO₂] in which fossil leaves developed. Many studies have investigated stomatal physiology or morphology in isolation, which may result in the loss of the ‘overall picture’ as these traits operate in a coordinated manner to produce distinct mechanisms for stomatal control. Consideration of the interaction between stomatal morphology and physiology is critical to our understanding of plant evolutionary history, plant responses to on-going climate change and the production of more efficient and climate-resilient food and bio-fuel crops.

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]

As atmospheric [CO₂] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO₂ (eCO₂) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO₂. Although many genes were found to be commonly expressed by the two genotypes under eCO₂, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO₂. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO₂ with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO₂ in these coffee genotypes.

The methylome is altered for plants in a high CO2 world: Insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO2 ]

Unravelling plant responses to rising atmospheric CO₂ concentration ([CO₂ ]) has largely focussed on plastic functional attributes to single generation [CO₂ ] exposure. Quantifying the consequences of long-term, decadal multigenerational exposure to elevated [CO₂ ] and the genetic changes that may underpin evolutionary mechanisms with [CO₂ ] as a driver remain largely unexplored. Here, we investigated both plastic and evolutionary plant responses to elevated [CO₂ ] by applying multi-omic technologies using populations of Plantago lanceolata L., grown in naturally high [CO₂ ] for many generations in a CO₂ spring. Seed from populations at the CO₂ spring and an adjacent control site (ambient [CO₂ ]) were grown in a common environment for one generation, and then offspring were grown in ambient or elevated [CO₂ ] growth chambers. Low overall genetic differentiation between the CO₂ spring and control site populations was found, with evidence of weak selection in exons. We identified evolutionary divergence in the DNA methylation profiles of populations derived from the spring relative to the control population, providing the first evidence that plant methylomes may respond to elevated [CO₂ ] over multiple generations. In contrast, growth at elevated [CO₂ ] for a single generation induced limited methylome remodelling (an order of magnitude fewer differential methylation events than observed between populations), although some of this appeared to be stably transgenerationally inherited. In all, 59 regions of the genome were identified where transcripts exhibiting differential expression (associated with single generation or long-term natural exposure to elevated [CO₂ ]) co-located with sites of differential methylation or with single nucleotide polymorphisms exhibiting significant inter-population divergence. This included genes in pathways known to respond to elevated [CO₂ ], such as nitrogen use efficiency and stomatal patterning. This study provides the first indication that DNA methylation may contribute to plant adaptation to future atmospheric [CO₂ ] and identifies several areas of the genome that are targets for future study.

A rice small GTPase, Rab6a, is involved in the regulation of grain yield and iron nutrition in response to CO2 enrichment

Despite extensive studies on the effects of elevated atmospheric CO2 concentrations ([CO2]) on rice, the molecular mechanisms and signaling events underlying the adaptation of plants remain largely elusive. Here, we report that OsRab6a, which encodes a small GTPase, is involved in the regulation of rice growth, grain yield, and accumulation of iron (Fe) in response to elevated [CO2] (e[CO2]). We generated transgenic plants with OsRab6a-overexpression (-OE) together with OsRab6a-RNAi lines, and found no differences in growth and grain yield among them and wild-type (WT) plants under ambient [CO2] conditions. Under e[CO2] conditions, growth and grain yield of the WT and OsRab6a-OE plants were enhanced, with a greater effect being observed in the latter. In contrast, there were no effects of e[CO2] on growth and grain yield of the OsRab6a-RNAi plants. Photosynthetic rates in both the WT and OsRab6a-OE plants were stimulated by e[CO2], with the magnitude of the increase being higher in OsRab6a-OE plants. Fe concentrations in vegetative tissues and the grain of the WT and transgenic plants were reduced by e[CO2], and the magnitude of the decrease was lower in the OE plants than in the WT and RNAi plants. Genes associated with Fe acquisition in the OsRab6a-OE lines exhibited higher levels of expression than those in the WT and the RNAi lines under e[CO2]. Analysis of our data using Dunnett's multiple comparison test suggested that OsRab6a is an important molecular regulator that underlies the adaptation of rice to e[CO2] by controlling photosynthesis and Fe accumulation.

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

Rye is used as food, feed, and for bioenergy production and remain an essential grain crop for cool temperate zones in marginal soils. Ergot is known to cause severe problems in cross-pollinated rye by contamination of harvested grains. The molecular response of the underlying mechanisms of this disease is still poorly understood due to the complex infection pattern. RNA sequencing can provide astonishing details about the transcriptional landscape, hence we employed a transcriptomic approach to identify genes in the underlying mechanism of ergot infection in rye. In this study, we generated de novo assemblies from twelve biological samples of two rye hybrids with identified contrasting phenotypic responses to ergot infection. The final transcriptome of ergot susceptible (DH372) and moderately ergot resistant (Helltop) hybrids contain 208,690 and 192,116 contigs, respectively. By applying the BUSCO pipeline, we confirmed that these transcriptome assemblies contain more than 90% of gene representation of the available orthologue groups at Virdiplantae odb10. We employed a de novo assembled and the draft reference genome of rye to count the differentially expressed genes (DEGs) between the two hybrids with and without inoculation. The gene expression comparisons revealed that 228 genes were linked to ergot infection in both hybrids. The genome ontology enrichment analysis of DEGs associated them with metabolic processes, hydrolase activity, pectinesterase activity, cell wall modification, pollen development and pollen wall assembly. In addition, gene set enrichment analysis of DEGs linked them to cell wall modification and pectinesterase activity. These results suggest that a combination of different pathways, particularly cell wall modification and pectinesterase activity contribute to the underlying mechanism that might lead to resistance against ergot in rye. Our results may pave the way to select genetic material to improve resistance against ergot through better understanding of the mechanism of ergot infection at molecular level. Furthermore, the sequence data and de novo assemblies are valuable as scientific resources for future studies in rye.

Implications of elevated carbon dioxide on the susceptibility of the globally invasive weed, Parthenium hysterophorus, to glyphosate herbicide

BACKGROUND

The noxious annual herb, Parthenium hysterophorus L. (Asteraceae), is an invasive weed of global significance, threatening food security, biodiversity and human health. In South Africa, chemical control is frequently used to manage P. hysterophorus, however, concern surrounds increasing atmospheric CO2 levels, which may reduce the efficacy of glyphosate against the weed. Therefore, this study aimed to determine the susceptibility of P. hysterophorus to glyphosate (1L/ha: recommended) after being grown for five generations in Convirons under ambient (400 ppm) and elevated (600 and 800 ppm) CO2 .

RESULTS

Glyphosate efficacy decreased with increasing CO2 , with mortalities of 100, 83 and 75% recorded at 400, 600 and 800 ppm, respectively. Parthenium hysterophorus experienced enhanced growth and reproduction under elevated CO2, however, glyphosate application was highly damaging, reducing the growth and flowering of plants across all CO2 treatments. Physiologically, glyphosate-treated plants, in all CO2 treatments, suffered severe declines of >90% in chlorophyll content, maximum quantum efficiency (F v /Fm ), photon absorption (ABS/RC), electron transport (ET 0 /RC) and performance index (PI ABS ), albeit at slower rates for plants grown under elevated CO2 . Low levels of recovery from glyphosate were documented only for plants grown under elevated CO2 and was attributed to their increased biomass.

CONCLUSION

These results suggest that increasing CO2 levels may hinder chemical control efforts used against P. hysterophorus in the future, advocating for further investigation using multigenerational CO2 studies and the maintenance of effective spraying programs at present. © 2020 Society of Chemical Industry.

Leaf ecophysiological and metabolic response in Quercus pyrenaica Willd seedlings to moderate drought under enriched CO2 atmosphere

Impact of drought under enriched CO₂ atmosphere on ecophysiological and leaf metabolic response of the sub-mediterranean Q. pyrenaica oak was studied. Seedlings growing in climate chamber were submitted to moderate drought (WS) and well-watered (WW) under ambient ([CO₂]_amb =400 ppm) or CO₂ enriched atmosphere ([CO₂]_enr =800 ppm). The moderate drought endured by seedlings brought about a decrease in leaf gas exchange. However, net photosynthesis (A_net) was highly stimulated for plants at [CO₂]_enr. There was a decrease of the stomatal conductance to water vapour (g_wv) in response to drought, and a subtle trend to be lower under [CO₂]_enr. The consequence of these changes was an important increase in the intrinsic leaf water use efficiency (WUEi). The electron transport rate (ETR) was almost a 20 percent higher in plants at [CO₂]_enr regardless drought endured by seedlings. The ETR/A_net was lower under [CO₂]_enr, pointing to a high capacity to maintain sinks for the uptake of extra carbon in the atmosphere. Impact of drought on the leaf metabolome, as a whole, was more evident than that from [CO₂] enrichment of the atmosphere. Changes in pool of non-structural carbohydrates were observed mainly as a consequence of water deficit including increases of fructose, glucose, and proto-quercitol. Most of the metabolites affected by drought back up to levels of non-stressed seedlings after rewetting (recovery phase). It can be concluded that carbon uptake was stimulated by [CO₂]_enr, even under the stomatal closure that accompanied moderate drought. In the last, there was a positive effect in intrinsic water use efficiency (WUEi), which was much more improved under [CO₂]_enr. Leaf metabolome was little responsible and some few metabolites changed mainly in response to drought, with little differences between [CO₂] growth conditions.

Two reproductive traits show contrasting genetic architectures in Plantago lanceolata

In many species, temperature-sensitive phenotypic plasticity (i.e., an individual's phenotypic response to temperature) displays a positive correlation with latitude, a pattern presumed to reflect local adaptation. This geographical pattern raises two general questions: (a) Do a few large-effect genes contribute to latitudinal variation in a trait? (b) Is the thermal plasticity of different traits regulated pleiotropically? To address the questions, we crossed individuals of Plantago lanceolata derived from northern and southern European populations. Individuals naturally exhibited high and low thermal plasticity in floral reflectance and flowering time. We grew parents and offspring in controlled cool- and warm-temperature environments, mimicking what plants would encounter in nature. We obtained genetic markers via genotype-by-sequencing, produced the first recombination map for this ecologically important nonmodel species, and performed quantitative trait locus (QTL) mapping of thermal plasticity and single-environment values for both traits. We identified a large-effect QTL that largely explained the reflectance plasticity differences between northern and southern populations. We identified multiple smaller-effect QTLs affecting aspects of flowering time, one of which affected flowering time plasticity. The results indicate that the genetic architecture of thermal plasticity in flowering is more complex than for reflectance. One flowering time QTL showed strong cytonuclear interactions under cool temperatures. Reflectance and flowering plasticity QTLs did not colocalize, suggesting little pleiotropic genetic control and freedom for independent trait evolution. Such genetic information about the architecture of plasticity is environmentally important because it informs us about the potential for plasticity to offset negative effects of climate change.

Transcriptome Reveals the Rice Response to Elevated Free Air CO2 Concentration and TiO2 Nanoparticles

Increasing CO₂ levels are speculated to change the effects of engineered nanomaterials in soil and on plant growth. How plants will respond to a combination of elevated CO₂ and nanomaterials stress has rarely been investigated, and the underlying mechanism remains largely unknown. Here, we conducted a field experiment to investigate the rice (Oryza sativa L. cv. IIyou) response to TiO₂ nanoparticles (nano-TiO₂, 0 and 200 mg kg^-1) using a free-air CO₂ enrichment system with different CO₂ levels (ambient ∼370 μmol mol^-1 and elevated ∼570 μmol mol^-1). The results showed that elevated CO₂ or nano-TiO₂ alone did not significantly affect rice chlorophyll content and antioxidant enzyme activities. However, in the presence of nano-TiO₂, elevated CO₂ significantly enhanced the rice height, shoot biomass, and panicle biomass (by 9.4%, 12.8%, and 15.8%, respectively). Furthermore, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that genes involved in photosynthesis were up-regulated while most genes associated with secondary metabolite biosynthesis were down-regulated in combination-treated rice. This indicated that elevated CO₂ and nano-TiO₂ might stimulate rice growth by adjusting resource allocation between photosynthesis and metabolism. This study provides novel insights into rice responses to increasing contamination under climate change.

Heritable Changes in Physiological Gas Exchange Traits in Response to Long-Term, Moderate Free-Air Carbon Dioxide Enrichment

Atmospheric carbon dioxide ([CO₂]) concentrations significantly alter developmental plant traits with potentially far-reaching consequences for ecosystem function and productivity. However, contemporary evolutionary responses among extant plant species that coincide with modern, anthropogenically driven [CO₂] rise have rarely been demonstrated among field-grown plant populations. Here we present findings from a long-term, free-air carbon dioxide enrichment (FACE) study in a seminatural European grassland ecosystem in which we observe a differential capacity among plant species to acclimate intrinsic water-use efficiencies (WUEs) in response to prolonged multigenerational exposure to elevated [CO₂] concentrations. In a reciprocal swap trial, using controlled environment growth chambers, we germinated seeds from six of the most dominant plant species at the FACE site [Arrhenatherum elatius (L.), Trisetum flavescens (L.), Holcus lanatus (L.), Geranium pratense (L.), Sanguisorba officinalis (L.), and Plantago lanceolata (L.)]. We found that long-term exposure to elevated [CO₂] strongly influenced the dynamic control of WUE_i in the first filial generations (F₁) of all species as well as an unequal ability to adapt to changes in the [CO₂] of the growth environment among those species. Furthermore, despite trait-environment relationships of this nature often being considered evidence for local adaptation in plants, we demonstrate that the ability to increase WUE_i does not necessarily translate to an ecological advantage in diverse species mixtures.

De novo characterization of the Goji berry (Lycium barbarium L.) fruit transcriptome and analysis of candidate genes involved in sugar metabolism under different CO2 concentrations

Goji berry (Lycium barbarum L.) is one of the important economic crops due to its exceptional nutritional value and medicinal benefits. Although reduced sugar levels in goji berry exposed to long-term elevated carbon dioxide (CO2) have been documented, the underlying molecular mechanisms remain unknown. The objective of this study was to explore the transcriptome of goji berry fruit under ambient and elevated CO2 concentrations and further to screen the differentially expressed genes (DEGs) for functions related to sugar metabolism. Fruit samples from goji berry exposed to ambient (400 μmol mol-1) and elevated (700 μmol mol-1) levels of CO2 for 120 days were analyzed for total sugar, carotenoid and flavone analysis. In this study, a reduction in total sugar and carotenoid levels in the fruits grown under elevated CO2 levels were observed. Fruit samples were also used to construct cDNA libraries using a HiSeqTM2500 platform. Consequently, 81,100 unigenes were assembled, of which 35,111 (43.3%) were annotated using various databases. Through DEGs analysis, it was found that 55 genes were upregulated and 18 were down-regulated in response to elevated CO2 treatment. Genes involved in the sugar metabolism and the related pathways were identified by Gene Ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. Furthermore, three genes, LBGAE (Lycium barbarum UDP-glucuronate 4-epimerase), LBGALA (Lycium barbarum alpha-galactosidase) and LBMS (Lycium barbarum malate synthase), associated with sugar metabolism were identified and discussed with respect to the reduction in the total sugar levels along with the enzymes acid invertase (AI), sucrose synthase (SS) and sucrose phosphate synthase (SPS) of the sucrose metabolism. This study can provide gene sources for elucidating the molecular mechanisms of sugar metabolism in the fruit of goji berry under elevated CO2.

Evolutionary and ecological functional genomics, from lab to the wild

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

FACE facts hold for multiple generations; Evidence from natural CO2 springs

Rising atmospheric CO₂ concentration is a key driver of enhanced global greening, thought to account for up to 70% of increased global vegetation in recent decades. CO₂ fertilization effects have further profound implications for ecosystems, food security and biosphere-atmosphere feedbacks. However, it is also possible that current trends will not continue, due to ecosystem level constraints and as plants acclimate to future CO₂ concentrations. Future predictions of plant response to rising [CO₂ ] are often validated using single-generation short-term FACE (Free Air CO₂ Enrichment) experiments but whether this accurately represents vegetation response over decades is unclear. The role of transgenerational plasticity and adaptation in the multigenerational response has yet to be elucidated. Here, we propose that naturally occurring high CO₂ springs provide a proxy to quantify the multigenerational and long-term impacts of rising [CO₂ ] in herbaceous and woody species respectively, such that plasticity, transgenerational effects and genetic adaptation can be quantified together in these systems. In this first meta-analysis of responses to elevated [CO₂ ] at natural CO₂ springs, we show that the magnitude and direction of change in eight of nine functional plant traits are consistent between spring and FACE experiments. We found increased photosynthesis (49.8% in spring experiments, comparable to 32.1% in FACE experiments) and leaf starch (58.6% spring, 84.3% FACE), decreased stomatal conductance (g_s , 27.2% spring, 21.1% FACE), leaf nitrogen content (6.3% spring, 13.3% FACE) and Specific Leaf Area (SLA, 9.7% spring, 6.0% FACE). These findings not only validate the use of these sites for studying multigenerational plant response to elevated [CO₂ ], but additionally suggest that long-term positive photosynthetic response to rising [CO₂ ] are likely to continue as predicted by single-generation exposure FACE experiments.

Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics

Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.

Agroforestry: a sustainable environmental practice for carbon sequestration under the climate change scenarios-a review

Agroforestry is a sustainable land use system with a promising potential to sequester atmospheric carbon into soil. This system of land use distinguishes itself from the other systems, such as sole crop cultivation and afforestation on croplands only through its potential to sequester higher amounts of carbon (in the above- and belowground tree biomass) than the aforementioned two systems. According to Kyoto protocol, agroforestry is recognized as an afforestation activity that, in addition to sequestering carbon dioxide (CO₂) to soil, conserves biodiversity, protects cropland, works as a windbreak, and provides food and feed to human and livestock, pollen for honey bees, wood for fuel, and timber for shelters construction. Agroforestry is more attractive as a land use practice for the farming community worldwide instead of cropland and forestland management systems. This practice is a win-win situation for the farming community and for the environmental sustainability. This review presents agroforestry potential to counter the increasing concentration of atmospheric CO₂ by sequestering it in above- and belowground biomass. The role of agroforestry in climate change mitigation worldwide might be recognized to its full potential by overcoming various financial, technical, and institutional barriers. Carbon sequestration in soil by various agricultural systems can be simulated by various models but literature lacks reports on validated models to quantify the agroforestry potential for carbon sequestration.

CO2 studies remain key to understanding a future world

Contents 34 I. 34 II. 36 III. 37 IV. 37 V. 38 38 References 38 SUMMARY: Characterizing plant responses to past, present and future changes in atmospheric carbon dioxide concentration ([CO₂ ]) is critical for understanding and predicting the consequences of global change over evolutionary and ecological timescales. Previous CO₂ studies have provided great insights into the effects of rising [CO₂ ] on leaf-level gas exchange, carbohydrate dynamics and plant growth. However, scaling CO₂ effects across biological levels, especially in field settings, has proved challenging. Moreover, many questions remain about the fundamental molecular mechanisms driving plant responses to [CO₂ ] and other global change factors. Here we discuss three examples of topics in which significant questions in CO₂ research remain unresolved: (1) mechanisms of CO₂ effects on plant developmental transitions; (2) implications of rising [CO₂ ] for integrated plant-water dynamics and drought tolerance; and (3) CO₂ effects on symbiotic interactions and eco-evolutionary feedbacks. Addressing these and other key questions in CO₂ research will require collaborations across scientific disciplines and new approaches that link molecular mechanisms to complex physiological and ecological interactions across spatiotemporal scales.